Contacts of the helix formed by residues 244 - 270 (chain P) in PDB entry 2QJK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 244 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P THR 4.6 4.3 - - - -
33P ILE* 3.4 32.3 - - + +
34P MET 3.3 2.2 + - - -
35P ILE* 3.0 32.0 + - + +
37P THR* 4.0 7.2 - - - -
242P VAL 3.5 0.6 + - - -
243P PRO* 1.3 70.8 - - - +
245P TRP* 1.3 57.7 + - - +
247P TYR 3.2 0.7 + - - -
248P PHE* 2.7 70.0 + + + -
249P ILE* 3.4 21.4 + - + -
252P ASP* 3.9 4.9 - - - -
505P ANJ 3.4 77.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 245 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ILE* 3.2 27.6 + - + +
34P MET* 3.9 19.8 - - + +
243P PRO* 3.4 23.0 - - - +
244P PHE* 1.3 79.3 - - - +
246P PRO* 1.3 87.8 - - + +
247P TYR 3.4 0.7 - - - -
249P ILE* 3.7 40.4 - - + -
250P ILE* 5.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 246 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243P PRO* 4.8 1.1 - - + -
244P PHE 3.4 1.3 - - - -
245P TRP* 1.3 122.6 - - + +
247P TYR* 1.3 84.3 + - + +
248P PHE 3.4 2.0 - - - -
249P ILE* 4.0 0.9 - - + -
250P ILE* 3.0 33.6 + - + +
251Q LEU* 3.6 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 247 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242P VAL* 3.7 21.1 - - + -
243P PRO* 3.3 51.8 - - + +
244P PHE 3.2 1.0 + - - -
246P PRO* 1.3 88.4 - - + +
248P PHE* 1.3 63.2 + - - +
250P ILE* 3.9 2.6 - - - +
251P LYS 3.5 7.8 + - - -
251Q LEU* 3.1 49.5 + - + +
252Q TRP* 3.2 37.4 + + + +
254Q GLY 5.1 2.1 + - - -
255Q VAL* 3.7 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P THR* 3.2 34.5 - - + -
38P PRO 3.2 22.4 - - - -
39P ARG 4.6 1.1 - - - -
41P LEU* 3.7 20.2 - - + -
242P VAL* 4.0 11.2 - - + -
244P PHE* 2.7 52.1 + + + -
247P TYR* 1.3 72.2 - - - +
249P ILE* 1.3 55.7 + - - +
250P ILE 2.6 17.1 + - - -
251P LYS* 2.8 23.1 + - + -
252P ASP* 2.7 29.4 + - - +
505P ANJ 3.7 20.6 - + + -
252Q TRP* 3.6 24.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ILE* 3.3 31.0 - - + -
244P PHE* 3.4 23.8 + - + -
245P TRP* 3.7 42.8 - - + -
246P PRO 3.8 7.6 - - - +
248P PHE* 1.3 76.7 - - - +
250P ILE* 1.3 60.1 + - + +
252P ASP* 3.5 7.7 - - + +
253P VAL* 3.0 34.4 + - + +
505P ANJ 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 250 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245P TRP* 5.7 2.7 - - + -
246P PRO* 3.0 25.3 + - + +
247P TYR 3.9 2.9 - - - +
248P PHE 2.6 5.1 + - - -
249P ILE* 1.3 77.1 - - + +
251P LYS* 1.3 55.5 + - - +
252P ASP 3.0 0.9 - - - -
253P VAL* 2.9 8.1 + - + +
254P PHE 2.6 33.3 + - - -
244Q LEU* 4.6 12.2 - - + +
247Q THR* 4.1 22.7 - - + +
248Q ASN* 3.4 33.9 - - + +
251Q LEU* 3.7 23.6 - - + -
16R TYR* 6.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P LEU 3.7 22.2 + - - -
42P ASN* 4.1 9.9 + - - +
43P TRP* 3.1 42.7 - - + -
46P ILE* 4.9 4.3 - - - -
247P TYR 3.5 8.2 + - - +
248P PHE* 2.8 41.9 + - + +
250P ILE* 1.3 75.3 - - - +
252P ASP* 1.3 58.0 + - - +
254P PHE* 2.8 7.2 + - - +
255P ALA* 2.6 38.0 + - - +
505P ANJ 4.8 5.3 + - - -
248Q ASN* 3.4 23.2 + - - +
252Q TRP* 3.8 16.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ILE* 5.2 5.0 - - - +
49P VAL* 3.1 28.6 - - + +
244P PHE* 3.9 0.9 - - - -
248P PHE 2.7 22.5 + - - +
249P ILE* 3.5 8.3 - - + +
251P LYS* 1.3 76.2 - - - +
253P VAL* 1.3 54.3 + - + +
255P ALA* 3.3 4.7 + - - +
256P LEU* 2.7 39.2 + - - +
505P ANJ 2.6 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249P ILE* 3.0 24.0 + - + +
250P ILE* 2.9 9.1 + - + +
252P ASP* 1.3 80.3 - - + +
254P PHE* 1.3 64.9 + - - +
256P LEU* 3.3 15.0 + - + +
257P ALA* 3.0 22.1 + - + +
244Q LEU* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P TRP* 3.8 35.2 - + - -
250P ILE 2.6 16.7 + - - +
251P LYS* 2.8 9.8 + - - +
253P VAL* 1.3 76.8 - - - +
255P ALA* 1.3 66.5 + - - +
257P ALA* 3.1 13.7 + - - +
258P VAL* 3.3 29.1 + - + -
241Q SER* 3.7 21.8 - - - -
244Q LEU* 4.0 22.8 - - + +
245Q TYR* 3.9 42.0 - + + -
248Q ASN* 4.5 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P TRP* 4.5 8.7 - - + -
46P ILE* 3.8 42.0 - - + -
50P VAL* 6.0 0.4 - - + -
251P LYS 2.6 18.1 + - - +
252P ASP 3.7 2.7 - - - +
254P PHE* 1.3 74.5 - - - +
256P LEU* 1.3 65.1 + - - +
258P VAL* 2.7 24.7 + - - +
259P VAL* 2.9 17.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P VAL* 3.3 31.2 - - + -
50P VAL* 4.0 23.1 - - + +
53P PHE* 4.1 34.3 - - + -
252P ASP 2.7 20.4 + - - +
253P VAL* 3.3 16.6 - - + +
255P ALA* 1.3 72.2 - - - +
257P ALA* 1.3 56.4 + - - +
259P VAL* 3.6 7.7 - - + +
260P LEU* 3.0 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253P VAL* 3.0 11.5 + - + +
254P PHE 3.2 11.0 - - - +
255P ALA 2.8 1.0 + - - -
256P LEU* 1.3 74.9 - - - +
258P VAL* 1.3 61.6 + - - +
260P LEU* 3.0 6.2 + - - +
261P LEU* 2.8 28.9 + - - +
237Q LEU* 4.0 18.3 - - + +
240Q LEU* 4.8 4.9 - - + -
241Q SER* 3.9 18.2 - - - +
244Q LEU* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 258 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254P PHE* 3.4 44.9 - - + +
255P ALA* 2.7 14.7 + - - +
257P ALA* 1.3 72.0 - - - +
259P VAL* 1.3 65.0 + - + +
261P LEU* 3.1 27.5 - - + +
262P VAL* 3.2 14.9 + - + +
241Q SER* 4.3 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ILE* 4.7 10.3 - - + -
47P TRP* 5.1 7.9 - - + -
50P VAL* 4.0 37.5 - - + -
103P LEU* 4.1 22.7 - - + -
255P ALA* 2.9 20.4 + - - +
256P LEU* 3.6 9.4 - - + +
258P VAL* 1.3 76.7 - - + +
260P LEU* 1.3 56.1 + - + +
262P VAL* 2.9 12.2 + - - +
263P PHE 2.8 29.6 + - - -
504P LOP 4.8 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P PHE* 3.3 53.8 - - + -
103P LEU* 4.9 4.9 - - + -
256P LEU* 3.0 32.4 + - + +
257P ALA* 3.5 5.8 - - - +
259P VAL* 1.3 78.6 - - + +
261P LEU* 1.3 58.6 + - - +
263P PHE* 3.7 21.3 - - + -
264P PHE* 2.6 54.4 + - + -
237Q LEU* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 261 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257P ALA 2.8 16.0 + - - +
258P VAL* 3.1 20.4 - - + +
260P LEU* 1.3 72.9 - - - +
262P VAL* 1.3 68.4 + - + +
264P PHE* 3.9 2.4 - - - +
265P ALA* 2.9 23.5 + - + +
234Q VAL* 3.4 44.3 - - + +
237Q LEU* 4.1 14.8 - - + +
238Q THR* 3.6 26.9 - - + +
241Q SER* 4.2 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258P VAL* 3.3 21.3 - - + +
259P VAL* 2.9 7.6 + - - +
261P LEU* 1.3 78.6 - - + +
263P PHE* 1.3 68.1 + - - +
265P ALA* 3.0 21.8 + - - +
266P ILE* 3.0 22.3 + - + +
504P LOP 4.4 27.6 - - + -
257Q BGL 4.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 263 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P PHE* 5.2 0.4 - + - -
57P LEU* 3.8 21.1 - - + -
96P LEU* 3.4 46.2 - - + -
99P ASN* 3.6 26.5 - - + -
100P GLY* 4.1 2.9 - - - -
103P LEU* 4.2 14.1 - - + -
259P VAL 2.8 17.1 + - - +
260P LEU* 3.1 28.7 + - + +
262P VAL* 1.3 71.8 - - - +
264P PHE* 1.3 74.3 + + - +
266P ILE* 2.9 12.8 + - - +
267P VAL* 2.9 30.9 + - + +
504P LOP 3.6 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 264 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P PHE* 5.6 3.4 - + - -
57P LEU* 6.5 0.4 - - + -
92P MET* 5.5 9.6 - - - -
96P LEU* 4.1 33.0 - - + -
260P LEU* 2.6 49.2 + - + +
261P LEU 3.9 2.5 - - - +
263P PHE* 1.3 82.8 - + - +
265P ALA* 1.3 53.6 + - - +
267P VAL* 3.4 7.5 - - + +
268P GLY* 2.5 37.2 + - - -
230Q GLY* 5.4 2.7 - - - -
233Q ALA* 3.8 31.0 - - + -
234Q VAL* 5.2 2.2 - - + +
237Q LEU* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 265 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261P LEU* 2.9 16.3 + - + +
262P VAL* 3.0 19.3 - - - +
264P PHE* 1.3 75.2 - - - +
266P ILE* 1.3 51.4 + - - +
269P PHE* 2.7 53.7 + - + +
270P MET* 5.3 0.2 - - - -
234Q VAL* 4.6 9.8 - - + +
257Q BGL 4.5 27.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 266 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P ASN* 4.1 16.4 - - - +
262P VAL* 3.0 26.7 + - + +
263P PHE* 2.9 8.7 + - - +
265P ALA* 1.3 73.9 - - + +
267P VAL* 1.3 63.8 + - + +
268P GLY 3.0 1.6 - - - -
270P MET* 2.6 80.9 + - + +
271P PRO 2.9 0.7 - - - -
273P TYR* 5.4 0.9 - - + -
274P LEU* 5.1 7.6 - - + -
504P LOP 4.4 26.5 - - + -
257Q BGL 5.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P MET* 4.4 12.9 - - - +
95P TYR* 3.9 26.1 - - + +
96P LEU* 3.9 26.0 - - + +
99P ASN* 4.3 7.4 - - + +
263P PHE* 2.9 51.1 + - + +
264P PHE* 3.7 10.8 - - + +
266P ILE* 1.3 74.4 - - + +
268P GLY* 1.3 62.2 + - - +
271P PRO* 3.7 19.2 - - - +
226Q ARG* 4.0 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P MET* 5.3 3.4 - - - -
264P PHE 2.5 20.8 + - - -
265P ALA 3.8 0.2 - - - -
267P VAL* 1.3 75.1 - - - +
269P PHE* 1.3 65.6 + - - +
226Q ARG* 3.0 47.0 + - - +
227Q LYS* 4.5 1.7 - - - +
230Q GLY* 4.5 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265P ALA* 2.7 35.5 + - + +
268P GLY* 1.3 78.2 - - - +
270P MET* 1.3 58.5 + - - +
271P PRO* 3.6 4.4 - - - +
16Q PRO* 3.6 44.4 - - + -
226Q ARG* 4.0 5.1 + - - +
227Q LYS* 4.1 20.6 - - + +
230Q GLY* 4.2 5.8 - - - -
231Q PHE* 3.8 38.4 - + - -
234Q VAL* 4.2 22.2 - - + -
257Q BGL 2.8 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 270 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P ASN* 4.7 0.2 - - - +
266P ILE* 2.6 54.8 + - + +
269P PHE* 1.3 77.4 - - + +
271P PRO* 1.3 65.2 - - - +
272P ASN 3.2 2.2 - - - -
273P TYR* 3.2 46.1 + - + +
121Q LEU* 3.6 38.8 - - + +
257Q BGL 4.1 34.3 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il